The way that I "thought" Blender worked is that if you had multiple render layers checked, Blender would automatically render all those render layers and then you could switch between those render layers in the UV/Image Editor and save the ones that you want or save all of them.
Now unless I am experiencing some kind of bug, this is not the way Blender works. What I would like to know is how I can set up Render Layer 1 to have Film>Transparent enabled so I get the alpha channel where it is masked and then to have Film>Transparent disabled for Render Layer 2 so I get the background showing and then to press Render and have both render layers produced for me in one shot as opposed to having to setup and render Render Layer 1 and then afterwards, uncheck Render Layer 1 and setup Render Layer 2 and then render again.
Is there a way of doing this natively in Blender or is there an add-on that does this? Is it just me or is it confusing that Blender lets you have multiple Render Layers enabled but it only renders the first enabled render layer?
Thanks to anyone who can clear up my confusion. BTW..I am rendering a single image and not an animation.